quickUMLSEndpoint/README at main · scottjpearson/quickUMLSEndpoint · GitHub

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INSTALL IN THIS DIRECTORY:
1> git clone git@github.com:Georgetown-IR-Lab/QuickUMLS.git
   Guide: https://github.com/Georgetown-IR-Lab/QuickUMLS?tab=readme-ov-file
2> cd QuickUMLS
3. Get a license from NLM at https://uts.nlm.nih.gov/license.html
4. Download all UMLS files from
   https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html
5. Install UMLS using the MetamorphoSys tool:
   https://www.nlm.nih.gov/pubs/factsheets/umlsmetamorph.html
   Guide:
   https://www.nlm.nih.gov/research/umls/implementation_resources/metamorphosys/help.html
6> conda activate 3.11
7> conda install anaconda::medspacy_quickumls
8> python -m spacy download en_core_web_sm
9. Install leveldb on your system, which has different installation requirements
   for each OS. I had success on MacOS by installing it via Homebrew and then running:
      > pip install leveldb-py
10> pip install quickumls-simstring
11> python -m quickumls.install 2025AA/META QuickUMLS.db
12> cd ..


INITIALIZE SERVER:
1> cd QuickUMLS
2> python -m quickumls.server QuickUMLS.db &
3> cd ..
4> python server.py &
The server will be started on port 8081.


USING THE SERVER:
1. Change your localhost to your IP/server in the following JavaScript.
2. Change $('#text').val() to your input string.
3. Change // PROCESS YOUR DATA HERE to use the JSON.

    function fetchJSON() {
      $('#result').html('');
      const json = JSON.stringify({ text: $('#text').val() });
      console.log(json);
      fetch("http://localhost:8081", {method:'POST', headers:{
          'content-type': 'application/json',
          'Content-Length': json.length
        },
        'body': json
      })
        .then(response => response.json())
        .then(data => {
             console.log(JSON.stringify(data));
             // PROCESS YOUR DATA HERE
        })
        .catch(error => console.error(error));
    }


NOTES:
- Need to convert curly quotes into normal quotes!
- To get rid of acronyms, use OpenAI with the following phrase as a pre-screen:
Please expand the medical acronyms in the following text without any commentary: XXXXXXXX
E.g., Please expand the medical acronyms in the following text without any commentary: To support young investigators conducting clinical research studies in ALS.